Having recently made the switch to the manual folder-based installation of mods, I must say that I do miss the Wrye Bash functionality which can merge your level lists and highlight file conflicts, so getting those back would be excellent. (Incorporating other features, such as Mlox sorting and Wrye Bash's "lock edit times" so that you can edit plugins without adjusting their creation dates, would be even better!)

That said, the manual folders are otherwise a really quick, clean and easy way of installing mods, provided that you remember that folders that load after other folders win priority in file conflicts. (Folder order is also separate to esp order.)